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https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29115
Rhizosphere Interactions
2008-03-15T16:13:30Z
<p>Jbaumgartel: </p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rhizoplane are closer to the actual roots than the microbes in the rhizosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rhizoplane than in the more loosely assoicated rhizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rhizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
*F. Martin, A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rusty J Rodriguez, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29114
Rhizosphere Interactions
2008-03-15T16:11:53Z
<p>Jbaumgartel: </p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rhizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rhizoplane than in the more loosely assoicated rhizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rhizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
*F. Martin, A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rusty J Rodriguez, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29113
Rhizosphere Interactions
2008-03-15T16:10:29Z
<p>Jbaumgartel: </p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rhizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rhizoplane than in the more loosely assoicated rhizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rhizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====pH====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
the availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
*F. Martin, A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rusty J Rodriguez, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28960
Rhizosphere Interactions
2008-03-14T21:37:44Z
<p>Jbaumgartel: </p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====pH====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
the availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28959
Rhizosphere Interactions
2008-03-14T21:36:55Z
<p>Jbaumgartel: </p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====pH====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
the availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28958
Rhizosphere Interactions
2008-03-14T21:36:33Z
<p>Jbaumgartel: </p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====pH====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
the availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Talk:Nitrogen_Cycle&diff=28957
Talk:Nitrogen Cycle
2008-03-14T21:34:37Z
<p>Jbaumgartel: </p>
<hr />
<div>In the contents section, microorganism is spelled "microoraganisms".<br />
<br />
It might be nice to have links to microorganisms in each of the sections. [user jbaumgartel]<br />
<br />
Very impressive~!!. But I'd like to suggest one thing. You did not mention the reason why nitrous gas(N2O) is emitted during nitrification and denitrification. I think that you need to explain the reasons with '''leaky pipe''' model why nitric and nitrous oxside are released as side products of nitrification/denitrification [[User:Jokang|Sungho]] 16:56, 14 March 2008 (UTC)<br />
<br />
----<br />
Hi. Overall, I like the page. We have a link from our page (carbon cycle) to your page. "Microorganisms" is spelled incorrectly in all the headings. Seeing as there are no specific organisms listed in some of the "Key Microorganisms" sections, you should add some links or perhaps eliminate the sections altogether. Y'all did a great job on the current research section. I hope that Irina and Professor Scow like the page as much as I did![[User:Jmmullane|Jmmullane]] 06:09, 14 March 2008 (UTC)<br />
----<br />
<br />
In the introduction, it might be good to add other sources of ammonium that enter the system, like fertilizer or manure. N-fixation isn't the only ammonium entering many systems. Also, I think it is misleading to say the cycle begins and stops at a given substance. The nitrogen cycle is just that, a cycle. <br />
<br />
Look over the Intro again- atmospheric N2 is inorganic. It is converted to organic N when it is fixed and amino acids / nucleic acids are synthesized. <br />
<br />
You say N2 is "unavailable for biological activity due to the high energy required to break the triple bond." This is incorrect. If N2 was biologically unavailable, no fixation would occur and the cycle would come to a halt. The fact that some organisms can fix N means it is biologically available to them, albeit at a significant energy cost.<br />
<br />
"Nitrogen mineralization is the sum of concurrent ammonium production and consumption processes." Net mineralization may be the sum of ammonium production and consumption, but mineralization in general refers to NH4 release from the cells. <br />
[[User:Icclark|Icclark]] 05:32, 14 March 2008 (UTC) <br />
----<br />
<br />
You should check and make sure that all microbe names are italicized and capitalized (except specific epithet. I noticed 2 in the intro that need it. you italicize by putting two apostrophes at either end of the word like ''so'' [[User:Njblackburn|Njblackburn]] 04:19, 14 March 2008 (UTC)<br />
----<br />
<br />
Also, I was a bit confused by "The nitrogen cycle begins when atmospheric N2 is transformed by organisms to NH4. This process is known as mineralization, when organic nitrogen is transformed into inorganic nitrogen." N<sub>2</sub> isn't organic, is it? and mineralization is the conversion of organic N to NH<sub>4</sub>, with fixation being the conversion of atmospheric N to orgaqnic N (mineralization isn't the whole conversion of atmospheric N<sub>2</sub> to NH<sub>4</sub>).[[User:Njblackburn|Njblackburn]] 04:29, 14 March 2008 (UTC)<br />
----<br />
Good catch NJ, i fixed it and added nitrogen cycle starts with nitrogen fixation, etc, etc. [[User:Njppatel|Njppatel]] 06:41, 14 March 2008 (UTC)<br />
----<br />
Hi N-people! Overall good lookin’ page! I have copied and pasted sentences from your section to this discussion board and added comments so you can better understand my comments: <br />
first section: “Denitrification is when nitrate gets converted into atmospheric nitrogen which is a greenhouse gas.” Not all forms of atmospheric N are greenhouse gases- I would clarify this.<br />
Nitrogen cycle processes:” Nitrogen is an essential nutrient for all life on earth. It is present in various forms such as dinitrogen gas, organic nitrogen, and ammonium and nitrate ions.” -nitrous oxide? nitric oxide? nitrite? I would suggest including all N forms in this list or maybe rephrase the sentence- slightly misleading.<br />
“Nitrogen mineralization is the sum of concurrent ammonium production and consumption processes.”-is this correct? (in terms of defining mineralization?)<br />
For the section on denitrification, I think you need to elaborate a bit on how nitrous oxide is released into the atmosphere since it’s not in the chemical formula for that section. Does nitrate go directly to N2?<br />
“Denitrification reduces the amount of nitrate from the environment by converting it into atmospheric nitrogen which is a greenhouse gas.”- again, not all atmospheric N is a ghg. maybe just clarify?<br />
I agree with the others about C:N 20-30 boundary stuff. Maybe just rephrase so it’s a little less of a concrete-boundary?<br />
Overall really good job, Heather<br />
-----------------------------------------<br />
Very nice work people. I think you really broke it down well for people that might be unfamiliar with the topic. In terms of the C/N discussion I agree with Kate in that some how it should be incorporated into immobilization and mineralization. Another thing with the C/N stuff is that the values that Kate gave (you know like <20 and >30) I am pretty sure are just generalizations. It would be good to note that in your discussion so that it is clear that these are not hard and fast numbers. Other than that there are some sentence level things that I think you could clear up by just reading through it and editing it for grammar and even some spelling and punctuation. The last thing would be some other formatting to make it clear what the subheadings and superheadings are (maybe adding numbers like 1,2,3 to the superheadings or some other clear distinction) because with the way it is set up now with the template the only distinction is a little bit smaller font. In terms of formatting, one last, last thing is to make sure your general template is the same, so for instance if you choose to use a "chemistry" subheading for the location of chemical reactions then have that be the same for each superheading. Over all great job though guys!!![[User:Kjmuzikar|Kjmuzikar]] 23:25, 13 March 2008 (UTC)<br />
----<br />
Okay cool thanks,i changed the c/n ratio to match what your are talking about thanks [[User:Njppatel|Njppatel]] 06:38, 14 March 2008 (UTC)<br />
----<br />
Awesome page guys! It was a fun read. I especially like the image for "N Cycle Showing Aerobic and Anaerobic Processes". Though over-simplified, it does demonstrate well the over-all big picture. I agree with Paul: "you really know your N!" [[User:Lapeacock|Leslie Peacock]] 09:40, 13 March 2008 (UTC)<br />
----<br />
Thank you for the compliment Leslie[[User:Njppatel|Njppatel]] 18:54, 13 March 2008 (UTC)<br />
----<br />
<br />
Great job! Under the Nitrogen Fixation section, I would suggest expanding on the Key Microorganisms by name dropping a few microbes that have exhibited the ability to fix nitrogen. I would suggest mentioning: [[Rhizobium]], [[Bradyrhizobium]] and [[Azotobacter]]. [[User:Sdemetriou|Sdemetriou]] 07:28, 13 March 2008 (UTC)<br />
----<br />
Hmmm that would be a good idea, i will look into adding those n fixers into the section, Ok it has been fixed under the nitrogen fixation section thanks again for input[[User:Njppatel|Njppatel]] 18:54, 13 March 2008 (UTC)<br />
----<br />
I suggested putting 2.4 as a subheading under 2.3 though now I see it is about both mineralization and immobilization. I still think it is a little odd to have it called out as its own heading after these 2 processes. Perhaps you could include it within mineralization section and not as heading. Or you could combine mineral/immob and have C/N as first subsection. It is up to you folks, though.<br />
<br />
[[User:Kmscow|Kate Scow]] 15:18, 11 March 2008 (UTC)<br />
----<br />
It is really an issue assocdo you really mean, under environmental concerns, that nitrificatoin has POSITIVE impacts on groundwater pollution. Seems like negative impact to me.<br />
[[User:Kmscow|Kate Scow]] 07:22, 11 March 2008 (UTC)<br />
----<br />
<br />
Most of nitrogen cycle related microbes are popular and already created in wiki.However,I create a new microbe page at http://microbewiki.kenyon.edu/index.php/Thiomicrospira_denitrificans. Let check it. [[User:Tantayotai|Tantayotai]] 00:39, 11 March 2008 (UTC)<br />
<br />
Wow, good job Tee. Make sure to add the new page to your watchlist so you get notified on comments. [[User:Irina.chakraborty|Irina C]] 01:03, 11 March 2008 (UTC)<br />
<br />
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<br />
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<br />
<br />
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Good start. A couple of comments. N cycle is biogeochemical not just chemical cycle. Also add that nitrate is then converted to N2 gas and then everything repeats itself. <br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
<br />
Great start! See if you can find some key nitrogen cycle organisms on the microbewiki and create links to their pages. Then start a page for a new microbe by using the code of an existing page as a template and editing the content. Remember to cite your sources!<br />
<br />
[[User:Irina.chakraborty|Irina C]] 21:45, 10 February 2008 (UTC)<br />
----<br />
I would suggest putting the microbes involved under each subheading. you can have nitrosomonas/nitrobacter and archaea under nitrification. Facultative anaerobes under denitr. Just mention breadth of organisms involved in immob/mineralization and why there is that breadth.<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
For global warming, you can find lots of good links for greenhouse gases. One good one would be good.<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
Remember to cite references for your information, especially for somewhat unique info (like alternative nitrogenases)<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
----<br />
hi, you really know your N! <br />
looks real good. I was going to suggest considering "Introduction" for #1. -Paul W<br />
----<br />
<br />
I would suggest putting C/N ratio under the category of immobilization as it is a subtopic of this process.<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
as mentioned early, the relevant organisms sections could be more developed. This goes for our page as well, because it takes some time. the pictures you have at the top really add to initial appearance of the page. perhaps include a picture in the relevant microbes section so that the viewers interest is rekindled in the lower part of your page. congrats on the good work, keep it up! [[User:Pbwebb|Pbwebb]] 04:22, 14 March 2008 (UTC) ----</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Talk:Nitrogen_Cycle&diff=28956
Talk:Nitrogen Cycle
2008-03-14T21:31:52Z
<p>Jbaumgartel: </p>
<hr />
<div>It might be nice to have links to microorganisms in each of the sections. [user jbaumgartel]<br />
<br />
Very impressive~!!. But I'd like to suggest one thing. You did not mention the reason why nitrous gas(N2O) is emitted during nitrification and denitrification. I think that you need to explain the reasons with '''leaky pipe''' model why nitric and nitrous oxside are released as side products of nitrification/denitrification [[User:Jokang|Sungho]] 16:56, 14 March 2008 (UTC)<br />
<br />
----<br />
Hi. Overall, I like the page. We have a link from our page (carbon cycle) to your page. "Microorganisms" is spelled incorrectly in all the headings. Seeing as there are no specific organisms listed in some of the "Key Microorganisms" sections, you should add some links or perhaps eliminate the sections altogether. Y'all did a great job on the current research section. I hope that Irina and Professor Scow like the page as much as I did![[User:Jmmullane|Jmmullane]] 06:09, 14 March 2008 (UTC)<br />
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<br />
In the introduction, it might be good to add other sources of ammonium that enter the system, like fertilizer or manure. N-fixation isn't the only ammonium entering many systems. Also, I think it is misleading to say the cycle begins and stops at a given substance. The nitrogen cycle is just that, a cycle. <br />
<br />
Look over the Intro again- atmospheric N2 is inorganic. It is converted to organic N when it is fixed and amino acids / nucleic acids are synthesized. <br />
<br />
You say N2 is "unavailable for biological activity due to the high energy required to break the triple bond." This is incorrect. If N2 was biologically unavailable, no fixation would occur and the cycle would come to a halt. The fact that some organisms can fix N means it is biologically available to them, albeit at a significant energy cost.<br />
<br />
"Nitrogen mineralization is the sum of concurrent ammonium production and consumption processes." Net mineralization may be the sum of ammonium production and consumption, but mineralization in general refers to NH4 release from the cells. <br />
[[User:Icclark|Icclark]] 05:32, 14 March 2008 (UTC) <br />
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<br />
You should check and make sure that all microbe names are italicized and capitalized (except specific epithet. I noticed 2 in the intro that need it. you italicize by putting two apostrophes at either end of the word like ''so'' [[User:Njblackburn|Njblackburn]] 04:19, 14 March 2008 (UTC)<br />
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<br />
Also, I was a bit confused by "The nitrogen cycle begins when atmospheric N2 is transformed by organisms to NH4. This process is known as mineralization, when organic nitrogen is transformed into inorganic nitrogen." N<sub>2</sub> isn't organic, is it? and mineralization is the conversion of organic N to NH<sub>4</sub>, with fixation being the conversion of atmospheric N to orgaqnic N (mineralization isn't the whole conversion of atmospheric N<sub>2</sub> to NH<sub>4</sub>).[[User:Njblackburn|Njblackburn]] 04:29, 14 March 2008 (UTC)<br />
----<br />
Good catch NJ, i fixed it and added nitrogen cycle starts with nitrogen fixation, etc, etc. [[User:Njppatel|Njppatel]] 06:41, 14 March 2008 (UTC)<br />
----<br />
Hi N-people! Overall good lookin’ page! I have copied and pasted sentences from your section to this discussion board and added comments so you can better understand my comments: <br />
first section: “Denitrification is when nitrate gets converted into atmospheric nitrogen which is a greenhouse gas.” Not all forms of atmospheric N are greenhouse gases- I would clarify this.<br />
Nitrogen cycle processes:” Nitrogen is an essential nutrient for all life on earth. It is present in various forms such as dinitrogen gas, organic nitrogen, and ammonium and nitrate ions.” -nitrous oxide? nitric oxide? nitrite? I would suggest including all N forms in this list or maybe rephrase the sentence- slightly misleading.<br />
“Nitrogen mineralization is the sum of concurrent ammonium production and consumption processes.”-is this correct? (in terms of defining mineralization?)<br />
For the section on denitrification, I think you need to elaborate a bit on how nitrous oxide is released into the atmosphere since it’s not in the chemical formula for that section. Does nitrate go directly to N2?<br />
“Denitrification reduces the amount of nitrate from the environment by converting it into atmospheric nitrogen which is a greenhouse gas.”- again, not all atmospheric N is a ghg. maybe just clarify?<br />
I agree with the others about C:N 20-30 boundary stuff. Maybe just rephrase so it’s a little less of a concrete-boundary?<br />
Overall really good job, Heather<br />
-----------------------------------------<br />
Very nice work people. I think you really broke it down well for people that might be unfamiliar with the topic. In terms of the C/N discussion I agree with Kate in that some how it should be incorporated into immobilization and mineralization. Another thing with the C/N stuff is that the values that Kate gave (you know like <20 and >30) I am pretty sure are just generalizations. It would be good to note that in your discussion so that it is clear that these are not hard and fast numbers. Other than that there are some sentence level things that I think you could clear up by just reading through it and editing it for grammar and even some spelling and punctuation. The last thing would be some other formatting to make it clear what the subheadings and superheadings are (maybe adding numbers like 1,2,3 to the superheadings or some other clear distinction) because with the way it is set up now with the template the only distinction is a little bit smaller font. In terms of formatting, one last, last thing is to make sure your general template is the same, so for instance if you choose to use a "chemistry" subheading for the location of chemical reactions then have that be the same for each superheading. Over all great job though guys!!![[User:Kjmuzikar|Kjmuzikar]] 23:25, 13 March 2008 (UTC)<br />
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Okay cool thanks,i changed the c/n ratio to match what your are talking about thanks [[User:Njppatel|Njppatel]] 06:38, 14 March 2008 (UTC)<br />
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Awesome page guys! It was a fun read. I especially like the image for "N Cycle Showing Aerobic and Anaerobic Processes". Though over-simplified, it does demonstrate well the over-all big picture. I agree with Paul: "you really know your N!" [[User:Lapeacock|Leslie Peacock]] 09:40, 13 March 2008 (UTC)<br />
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Thank you for the compliment Leslie[[User:Njppatel|Njppatel]] 18:54, 13 March 2008 (UTC)<br />
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<br />
Great job! Under the Nitrogen Fixation section, I would suggest expanding on the Key Microorganisms by name dropping a few microbes that have exhibited the ability to fix nitrogen. I would suggest mentioning: [[Rhizobium]], [[Bradyrhizobium]] and [[Azotobacter]]. [[User:Sdemetriou|Sdemetriou]] 07:28, 13 March 2008 (UTC)<br />
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Hmmm that would be a good idea, i will look into adding those n fixers into the section, Ok it has been fixed under the nitrogen fixation section thanks again for input[[User:Njppatel|Njppatel]] 18:54, 13 March 2008 (UTC)<br />
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I suggested putting 2.4 as a subheading under 2.3 though now I see it is about both mineralization and immobilization. I still think it is a little odd to have it called out as its own heading after these 2 processes. Perhaps you could include it within mineralization section and not as heading. Or you could combine mineral/immob and have C/N as first subsection. It is up to you folks, though.<br />
<br />
[[User:Kmscow|Kate Scow]] 15:18, 11 March 2008 (UTC)<br />
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It is really an issue assocdo you really mean, under environmental concerns, that nitrificatoin has POSITIVE impacts on groundwater pollution. Seems like negative impact to me.<br />
[[User:Kmscow|Kate Scow]] 07:22, 11 March 2008 (UTC)<br />
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<br />
Most of nitrogen cycle related microbes are popular and already created in wiki.However,I create a new microbe page at http://microbewiki.kenyon.edu/index.php/Thiomicrospira_denitrificans. Let check it. [[User:Tantayotai|Tantayotai]] 00:39, 11 March 2008 (UTC)<br />
<br />
Wow, good job Tee. Make sure to add the new page to your watchlist so you get notified on comments. [[User:Irina.chakraborty|Irina C]] 01:03, 11 March 2008 (UTC)<br />
<br />
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<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
* Add new comments to the TOP of the discussion page, so that we have newest comments first.<br />
* After your comment, type four tilde marks ( &#126;&#126;&#126;&#126; ). This displays the time and your user name, so that we can tell who left the comment and when.<br />
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* Make a note on this page below the comment after you've addressed it. Add the ( &#126;&#126;&#126;&#126; ) after your note so we know who addressed the comment. Your note could look something like .. "Good idea, we fixed it.[[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)" or "I don't think we need to do this because.. [[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)"<br />
<br />
<br />
----<br />
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Good start. A couple of comments. N cycle is biogeochemical not just chemical cycle. Also add that nitrate is then converted to N2 gas and then everything repeats itself. <br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
<br />
Great start! See if you can find some key nitrogen cycle organisms on the microbewiki and create links to their pages. Then start a page for a new microbe by using the code of an existing page as a template and editing the content. Remember to cite your sources!<br />
<br />
[[User:Irina.chakraborty|Irina C]] 21:45, 10 February 2008 (UTC)<br />
----<br />
I would suggest putting the microbes involved under each subheading. you can have nitrosomonas/nitrobacter and archaea under nitrification. Facultative anaerobes under denitr. Just mention breadth of organisms involved in immob/mineralization and why there is that breadth.<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
For global warming, you can find lots of good links for greenhouse gases. One good one would be good.<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
Remember to cite references for your information, especially for somewhat unique info (like alternative nitrogenases)<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
----<br />
hi, you really know your N! <br />
looks real good. I was going to suggest considering "Introduction" for #1. -Paul W<br />
----<br />
<br />
I would suggest putting C/N ratio under the category of immobilization as it is a subtopic of this process.<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
as mentioned early, the relevant organisms sections could be more developed. This goes for our page as well, because it takes some time. the pictures you have at the top really add to initial appearance of the page. perhaps include a picture in the relevant microbes section so that the viewers interest is rekindled in the lower part of your page. congrats on the good work, keep it up! [[User:Pbwebb|Pbwebb]] 04:22, 14 March 2008 (UTC) ----</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Talk:Soil_Environment&diff=28955
Talk:Soil Environment
2008-03-14T21:30:16Z
<p>Jbaumgartel: </p>
<hr />
<div>Hey, now you can link to the rhizosphere page that our group has created! [user jbaumgartel]<br />
<br />
It might be good to relate the information you have presented about soil texture back to the effect that it has on microbial life in the soil. [user jbaumgartel]<br />
<br />
Great job you guys!! I saw a lot of detail and new information. The only thing I saw wrong was that I believe you need three new studies and I only saw two. [user bhsparks]<br />
<br />
<br />
Soil water might be a subject worthy of a little more description. It seems like a rate limiting factor, one that governs microbial activity as well as mobility.<br />
<br />
A link in your Plant Growth-Promoting Rhizobacteria (PGPR)section to the Rhizosphere page would be nice. [[User:Icclark|Icclark]] 06:37, 14 March 2008 (UTC)<br />
----<br />
To get a subscript, do <sub>this</sub> [[User:Njblackburn|Njblackburn]] 04:51, 14 March 2008 (UTC)<br />
Great thanks. Didn't know that. Figured out superscript too![[User:Kjmuzikar|Kjmuzikar]] 05:21, 14 March 2008 (UTC)<br />
----<br />
<br />
In your intro you say "Microbial activity basically means the generation of microbial." microbial what?[[User:Njblackburn|Njblackburn]] 04:45, 14 March 2008 (UTC)<br />
----<br />
<br />
Hi everybody- great job overall. I have listed a few suggestions for your site:<br />
In the CEC section, I’m pretty sure soils (mineral surfaces) are negatively charged and microbes are positively charged. –It might be a good idea to just briefly define under each section soil texture, soil pores, and soil structure.—for the soil water section, you may want to include that it is a necessary habitat for some microbes (which types?).—for the temperature section, you have described Q10, you may want to introduce the term here.—You may want to combine the “soil structure” and “aggregate” section somehow.—You may want to change the section heading “PGRP” to just rhizobacteria, since you also have DRMO’s included in this section. <br />
I think some pictures would be great too. Heather <br />
<br />
Good broad covering of the subject. One suggestion I would have is possibly taking the information under "Organism Intertaions" and making a distinct chart. That way it's visually pleasing and sets the information apart. [[kamackey]]<br />
<br />
Maybe this could use some pictures? Maybe the organisms u talked about, or the rhizobia. Just something to make it pretty. -David La ````[[User:Dtla|Dtla]] 02:45, 14 March 2008 (UTC)<br />
<br />
I have heard that anion exchange capacity (not as significant as cec) can play a role in soil environments. If true you may want to add a short section regarding this.[[User:Njppatel|Njppatel]] 18:36, 13 March 2008 (UTC)<br />
----<br />
Also you may want to add a section about how aggregates get formed, other than that the information is great[[User:Njppatel|Njppatel]] 18:36, 13 March 2008 (UTC)<br />
----<br />
A suggestion: since you are looking at soil environ/physic factors, rather than a specific cycle or special environment, you get to be more creative with your relevant organisms. Some that I can think of, though, are ones that build soil structure (e.g. make polysaccharides, hyphae formers), as well as those extemophiles that tolerate really low and high pH, low and high temperature, osmotic extemists. Should be fun.<br />
[[User:Kmscow|Kate Scow]] 01:59, 10 March 2008 (UTC)<br />
----<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
* Add new comments to the TOP of the discussion page, so that we have newest comments first.<br />
* After your comment, type four tilde marks ( &#126;&#126;&#126;&#126; ). This displays the time and your user name, so that we can tell who left the comment and when.<br />
* At the end of your comment, type four hyphens "----" to create a line to separate your comment from the next commentator. <br />
* Make a note on this page below the comment after you've addressed it. Add the ( &#126;&#126;&#126;&#126; ) after your note so we know who addressed the comment. Your note could look something like .. "Good idea, we fixed it.[[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)" or "I don't think we need to do this because.. [[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)"<br />
----<br />
I suggest replacing microflora with "interactions with other microorganisms".----Kate Scow<br />
----<br />
Bioavailability :<br />
<br />
Definition of bioavailability is not quite right. You can go to book and lecture notes, or other sites, and develop better definition.---Kate<br />
----<br />
<br />
It seems your section on relevant microorganisms has disappeared. Please add it back and complete that part of the assignment. [[User:Irina.chakraborty|Irina C]] 02:42, 25 February 2008 (UTC)<br />
----<br />
<br />
Another thing, make sure to note down the sources of your information on the page as you write. You can format and link them as proper references later, but don't add any information without a citation to the source.<br />
<br />
To get subheadings, use various numbers of equal signs before and after the word (see template code).<br />
<br />
To actually create numbered lists, use the pound sign '#'. Different numbers of pound signs will create different levels of numbered text (click on Edit tab of this page to see):<br />
#Topic 1<br />
##Subtopic 1a<br />
##Subtopic 1b<br />
#Topic 2<br />
###etc<br />
####etc<br />
#####etc<br />
<br />
[[User:Irina.chakraborty|Irina C]] 18:48, 28 January 2008 (UTC)<br />
----<br />
<br />
Hi soil environment group. Please use section formats as in the template. You're the first group to start! great!!<br />
<br />
[[User:Irina.chakraborty|Irina C]] 04:58, 28 January 2008 (UTC)</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Talk:Soil_Environment&diff=28954
Talk:Soil Environment
2008-03-14T21:28:14Z
<p>Jbaumgartel: </p>
<hr />
<div>It might be good to relate the information you have presented about soil texture back to the effect that it has on microbial life in the soil. [user jbaumgartel]<br />
<br />
Great job you guys!! I saw a lot of detail and new information. The only thing I saw wrong was that I believe you need three new studies and I only saw two. [user bhsparks]<br />
<br />
<br />
Soil water might be a subject worthy of a little more description. It seems like a rate limiting factor, one that governs microbial activity as well as mobility.<br />
<br />
A link in your Plant Growth-Promoting Rhizobacteria (PGPR)section to the Rhizosphere page would be nice. [[User:Icclark|Icclark]] 06:37, 14 March 2008 (UTC)<br />
----<br />
To get a subscript, do <sub>this</sub> [[User:Njblackburn|Njblackburn]] 04:51, 14 March 2008 (UTC)<br />
Great thanks. Didn't know that. Figured out superscript too![[User:Kjmuzikar|Kjmuzikar]] 05:21, 14 March 2008 (UTC)<br />
----<br />
<br />
In your intro you say "Microbial activity basically means the generation of microbial." microbial what?[[User:Njblackburn|Njblackburn]] 04:45, 14 March 2008 (UTC)<br />
----<br />
<br />
Hi everybody- great job overall. I have listed a few suggestions for your site:<br />
In the CEC section, I’m pretty sure soils (mineral surfaces) are negatively charged and microbes are positively charged. –It might be a good idea to just briefly define under each section soil texture, soil pores, and soil structure.—for the soil water section, you may want to include that it is a necessary habitat for some microbes (which types?).—for the temperature section, you have described Q10, you may want to introduce the term here.—You may want to combine the “soil structure” and “aggregate” section somehow.—You may want to change the section heading “PGRP” to just rhizobacteria, since you also have DRMO’s included in this section. <br />
I think some pictures would be great too. Heather <br />
<br />
Good broad covering of the subject. One suggestion I would have is possibly taking the information under "Organism Intertaions" and making a distinct chart. That way it's visually pleasing and sets the information apart. [[kamackey]]<br />
<br />
Maybe this could use some pictures? Maybe the organisms u talked about, or the rhizobia. Just something to make it pretty. -David La ````[[User:Dtla|Dtla]] 02:45, 14 March 2008 (UTC)<br />
<br />
I have heard that anion exchange capacity (not as significant as cec) can play a role in soil environments. If true you may want to add a short section regarding this.[[User:Njppatel|Njppatel]] 18:36, 13 March 2008 (UTC)<br />
----<br />
Also you may want to add a section about how aggregates get formed, other than that the information is great[[User:Njppatel|Njppatel]] 18:36, 13 March 2008 (UTC)<br />
----<br />
A suggestion: since you are looking at soil environ/physic factors, rather than a specific cycle or special environment, you get to be more creative with your relevant organisms. Some that I can think of, though, are ones that build soil structure (e.g. make polysaccharides, hyphae formers), as well as those extemophiles that tolerate really low and high pH, low and high temperature, osmotic extemists. Should be fun.<br />
[[User:Kmscow|Kate Scow]] 01:59, 10 March 2008 (UTC)<br />
----<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
* Add new comments to the TOP of the discussion page, so that we have newest comments first.<br />
* After your comment, type four tilde marks ( &#126;&#126;&#126;&#126; ). This displays the time and your user name, so that we can tell who left the comment and when.<br />
* At the end of your comment, type four hyphens "----" to create a line to separate your comment from the next commentator. <br />
* Make a note on this page below the comment after you've addressed it. Add the ( &#126;&#126;&#126;&#126; ) after your note so we know who addressed the comment. Your note could look something like .. "Good idea, we fixed it.[[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)" or "I don't think we need to do this because.. [[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)"<br />
----<br />
I suggest replacing microflora with "interactions with other microorganisms".----Kate Scow<br />
----<br />
Bioavailability :<br />
<br />
Definition of bioavailability is not quite right. You can go to book and lecture notes, or other sites, and develop better definition.---Kate<br />
----<br />
<br />
It seems your section on relevant microorganisms has disappeared. Please add it back and complete that part of the assignment. [[User:Irina.chakraborty|Irina C]] 02:42, 25 February 2008 (UTC)<br />
----<br />
<br />
Another thing, make sure to note down the sources of your information on the page as you write. You can format and link them as proper references later, but don't add any information without a citation to the source.<br />
<br />
To get subheadings, use various numbers of equal signs before and after the word (see template code).<br />
<br />
To actually create numbered lists, use the pound sign '#'. Different numbers of pound signs will create different levels of numbered text (click on Edit tab of this page to see):<br />
#Topic 1<br />
##Subtopic 1a<br />
##Subtopic 1b<br />
#Topic 2<br />
###etc<br />
####etc<br />
#####etc<br />
<br />
[[User:Irina.chakraborty|Irina C]] 18:48, 28 January 2008 (UTC)<br />
----<br />
<br />
Hi soil environment group. Please use section formats as in the template. You're the first group to start! great!!<br />
<br />
[[User:Irina.chakraborty|Irina C]] 04:58, 28 January 2008 (UTC)</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28953
Rhizosphere Interactions
2008-03-14T21:20:14Z
<p>Jbaumgartel: /* Innoculants */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
the availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28952
Rhizosphere Interactions
2008-03-14T21:19:15Z
<p>Jbaumgartel: /* Innoculants */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
the availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[[Trichoderma harzianum]]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28951
Rhizosphere Interactions
2008-03-14T21:18:43Z
<p>Jbaumgartel: /* Innoculants */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
the availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonal syringae]]'' pv. ''tabaci''<br />
<br />
''[[Trichoderma harzianum]]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28950
Rhizosphere Interactions
2008-03-14T21:15:08Z
<p>Jbaumgartel: /* Innoculants */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
the availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[[Psuedomonas putida]]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonal syringae]]'' pv. ''tabaci''<br />
<br />
''[[Trichoderma harzianum]]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28949
Rhizosphere Interactions
2008-03-14T21:08:44Z
<p>Jbaumgartel: /* Innoculants */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
the availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
[''Agrobacterium tumefaciens'']<br />
<br />
''Alcaligenes'' spp.<br />
<br />
''Bacillus subtilis''<br />
<br />
''Azospirillum brasilense''<br />
<br />
''Pseudomonas fluorescens''<br />
<br />
''Psuedomonas putida''<br />
<br />
''Pseudomonas'' spp.<br />
<br />
''Pseudomonal syringae'' pv. ''tabaci''<br />
<br />
''Trichoderma harzianum''<br />
<br />
(Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28948
Rhizosphere Interactions
2008-03-14T21:08:17Z
<p>Jbaumgartel: /* Innoculants */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
the availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
[[''Agrobacterium tumefaciens'']]<br />
<br />
''Alcaligenes'' spp.<br />
<br />
''Bacillus subtilis''<br />
<br />
''Azospirillum brasilense''<br />
<br />
''Pseudomonas fluorescens''<br />
<br />
''Psuedomonas putida''<br />
<br />
''Pseudomonas'' spp.<br />
<br />
''Pseudomonal syringae'' pv. ''tabaci''<br />
<br />
''Trichoderma harzianum''<br />
<br />
(Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28947
Rhizosphere Interactions
2008-03-14T21:06:15Z
<p>Jbaumgartel: /* Innoculants */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
the availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''Agrobacterium tumefaciens''<br />
<br />
''Alcaligenes'' spp.<br />
<br />
''Bacillus subtilis''<br />
<br />
''Azospirillum brasilense''<br />
<br />
''Pseudomonas fluorescens''<br />
<br />
''Psuedomonas putida''<br />
<br />
''Pseudomonas'' spp.<br />
<br />
''Pseudomonal syringae'' pv. ''tabaci''<br />
<br />
''Trichoderma harzianum''<br />
<br />
(Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28508
Rhizosphere Interactions
2008-03-10T21:46:38Z
<p>Jbaumgartel: /* Innoculants */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allow the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28506
Rhizosphere Interactions
2008-03-10T21:14:27Z
<p>Jbaumgartel: /* References */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allow the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28504
Rhizosphere Interactions
2008-03-10T21:12:53Z
<p>Jbaumgartel: /* Biotic Interactions in the Rhizosphere */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allow the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28503
Rhizosphere Interactions
2008-03-10T21:11:19Z
<p>Jbaumgartel: /* General Impacts on Rhizosphere Microorganisms of Plants */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allow the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events.<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients.<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28502
Rhizosphere Interactions
2008-03-10T21:10:14Z
<p>Jbaumgartel: /* General Impacts on Plants of Rhizosphere Microorganisms */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allow the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events.<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants and rhizosphere microorganisms can also compete for resources like water and nutrients in the rhizosphere.<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28501
Rhizosphere Interactions
2008-03-10T21:03:39Z
<p>Jbaumgartel: /* Biotic Interactions in the Rhizosphere */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allow the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants.<br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient availability. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication during water stress events.<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants and rhizosphere microorganisms can also compete for resources like water and nutrients in the rhizosphere.<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28500
Rhizosphere Interactions
2008-03-10T20:58:33Z
<p>Jbaumgartel: /* General Impacts on Rhizosphere Microorganisms of Plants */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allow the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants.<br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient availability. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication during water stress events.<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants and rhizosphere microorganisms can also compete for resources like water and nutrients in the rhizosphere.<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28499
Rhizosphere Interactions
2008-03-10T20:41:18Z
<p>Jbaumgartel: /* General Impacts on Plants of Rhizosphere Microorganisms */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allow the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants.<br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient availability. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication during water stress events.<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28498
Rhizosphere Interactions
2008-03-10T20:40:39Z
<p>Jbaumgartel: /* General Impacts on Plants of Rhizosphere Microorganisms */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allow the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants.<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient availability. <br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication during water stress events.<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28497
Rhizosphere Interactions
2008-03-10T20:20:09Z
<p>Jbaumgartel: /* General Impacts on Plants of Rhizosphere Microorganisms */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allow the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile.<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=27285
Rhizosphere Interactions
2008-01-30T05:06:32Z
<p>Jbaumgartel: </p>
<hr />
<div>Template:Biorealm Soil Microbiology<br />
Contents<br />
[hide]<br />
<br />
* 1 List of topics<br />
* 2 Introduction<br />
* 3 Process - key points<br />
o 3.1 Subsection 1<br />
+ 3.1.1 Subsection 1a<br />
+ 3.1.2 Subsection 1b<br />
o 3.2 Subsection 2<br />
* 4 Key Microorganisms in ______<br />
* 5 Section 3<br />
* 6 Current Research<br />
* 7 References<br />
<br />
[edit] List of topics<br />
<br />
1. Nitrogen cycle including GHG<br />
2. Carbon cycle including GHG, decomp, soil OM<br />
3. Geomicrobiology - other elements<br />
4. Rhizosphere: environment and mycorrhizal fungi<br />
5. Soil environment and physical factors controlling microbial activity<br />
6. Flooded soils<br />
7. Bioremediation <br />
<br />
[edit] Introduction<br />
<br />
The point of this template is to give you a general idea of the layout of your page. You are not completely restricted to this format, so feel free to try out different things. We'll give you feedback as you work on your pages. Make sure to copy the "code" of this page to your own page before editing.<br />
<br />
Irina C<br />
<br />
Describe briefly the process you will address and the significance of soil microorganisms in the process (what functions do they perform?).<br />
[edit] Process - key points<br />
Populations of Soil Fauna<br />
Microflora Movement <br />
Plant-Microbe Interactions<br />
Describe the process, using as many sections/subsections as you require. Look at the list of other topics. Which involve processes similar to yours? Create links where relevant.<br />
[edit] Subsection 1<br />
[edit] Subsection 1a<br />
[edit] Subsection 1b<br />
[edit] Subsection 2<br />
[edit] Key Microorganisms in ______<br />
<br />
Identify and describe some microorganisms involved. Do they already have their own microbewiki pages? Add links. Create at least one page for a microbe relevant to your topic. Template will appear soon.<br />
[edit] Section 3<br />
<br />
Topic of your choice.<br />
[edit] Current Research<br />
<br />
Enter summaries of recent research here--at least three required<br />
[edit] References<br />
<br />
[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.<br />
<br />
Edited by student of Kate Scow</div>
Jbaumgartel
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=27284
Rhizosphere Interactions
2008-01-30T05:05:13Z
<p>Jbaumgartel: New page: Template:Biorealm Soil Microbiology Contents [hide] * 1 List of topics * 2 Introduction * 3 Process - key points o 3.1 Subsection 1 + 3.1.1 Subsectio...</p>
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<div>Template:Biorealm Soil Microbiology<br />
Contents<br />
[hide]<br />
<br />
* 1 List of topics<br />
* 2 Introduction<br />
* 3 Process - key points<br />
o 3.1 Subsection 1<br />
+ 3.1.1 Subsection 1a<br />
+ 3.1.2 Subsection 1b<br />
o 3.2 Subsection 2<br />
* 4 Key Microorganisms in ______<br />
* 5 Section 3<br />
* 6 Current Research<br />
* 7 References<br />
<br />
[edit] List of topics<br />
<br />
1. Nitrogen cycle including GHG<br />
2. Carbon cycle including GHG, decomp, soil OM<br />
3. Geomicrobiology - other elements<br />
4. Rhizosphere: environment and mycorrhizal fungi<br />
5. Soil environment and physical factors controlling microbial activity<br />
6. Flooded soils<br />
7. Bioremediation <br />
<br />
[edit] Introduction<br />
<br />
The point of this template is to give you a general idea of the layout of your page. You are not completely restricted to this format, so feel free to try out different things. We'll give you feedback as you work on your pages. Make sure to copy the "code" of this page to your own page before editing.<br />
<br />
Irina C<br />
<br />
Describe briefly the process you will address and the significance of soil microorganisms in the process (what functions do they perform?).<br />
[edit] Process - key points<br />
<br />
Describe the process, using as many sections/subsections as you require. Look at the list of other topics. Which involve processes similar to yours? Create links where relevant.<br />
[edit] Subsection 1<br />
[edit] Subsection 1a<br />
[edit] Subsection 1b<br />
[edit] Subsection 2<br />
[edit] Key Microorganisms in ______<br />
<br />
Identify and describe some microorganisms involved. Do they already have their own microbewiki pages? Add links. Create at least one page for a microbe relevant to your topic. Template will appear soon.<br />
[edit] Section 3<br />
<br />
Topic of your choice.<br />
[edit] Current Research<br />
<br />
Enter summaries of recent research here--at least three required<br />
[edit] References<br />
<br />
[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.<br />
<br />
Edited by student of Kate Scow</div>
Jbaumgartel